Tuesday, July 4, 2017

Cool science in June!

The humidity is high, fireworks are lighting up the sky, and the wonderful smells of charcoal and burgers fill the air. It's summer! But more importantly, it's time for a short review of some interesting science published in June. We'll start with tomatoes, because who doesn't love a burger with a slice of tomato?

Farmers and agriculturalists often select desired variants of a crop or other plant species they want to breed and further develop. Bigger tomatoes, new varieties of grapes for wine, drought-resistant wheat and barley, more potent strains of marijuana... there are hundreds of versions of many different plants. Gregor Mendel, the father of genetics, cultivated a handful of select traits in the pea plant (height, pea shape, and pea color to name a few) so that he could study the laws of inheritance.

When two desired versions of the same plant are combined together, say a drought-resistance variety of corn and a variety that grows bigger ears, the two can be bred together to get a super-variety: corn that yields larger ears AND is drought-resistant. But sometimes that combination of two desired traits develops nothing of value.

Such is the case with a few varieties of the tomato plant and researchers from around the world used CRISPR to study the molecular mechanisms that contributed to those undesirable outcomes. The authors were able to engineer a work-around to allow the new hybrid tomato plant to successfully grow and produce a higher yield of tomatoes compared with the two individual strains. This is an exciting use of CRISPR technology in food science and may better help us create crops that will still grow as our climate changes or allow these crops to resist insects and other pests. All of this is very important for our survival as a species.

But back in medicine, the controversies of CRISPR continue to develop. There was a brief article in Nature that presents evidence that CRISPR can cause off-target mutations in the genomes of mammalian cells. This is a really big deal, considering any therapy or gene-editing option using CRISPR will need to be 100% efficient in order to prevent mutations that could lead to diseases like cancer. This is one of the first papers specifically studying the off-target effects of the CRISPR gene-editing system. However, the results here need to be taken with a grain of salt as the authors only submitted their work on a small number of animals and they lacked a few important controls to fully support their conclusions.

Dr. George Church's research group uploaded a response to this article, pointing out the article's flaws, on the bioRxiv.org website. But this article also needs to be taken with a grain of salt, as the bioRxiv is a pre-peer review publication website. This means this manuscript has not been peer-reviewed nor is it published yet in a peer-review journal. So at best, Church's response can be called an opinion piece until it's formally published refuting the first article. (If you are interested in how the bioRxiv fits into the peer review process, please check out my blog post over at the Cosmic Roots website).

I'll comment that discourse like this is really great for the scientific field and hopefully spurs more interest in reproducing each lab's results. Researchers challenging another's work in a respectful way will help the technology advance. But until then we must all approach this with a healthy skepticism.

Okay, onto bacteria!

The human microbiome is an exploding topic in research these days.  Our gut bacteria can influence how we respond to the drugs that we take and our susceptibility to disease due to our diet. Additionally, bacteria on our skin can also influence our response to drugs and research is underway examining how that relationship impacts our everyday health. A new study studied the impact of the bacteria E. Coli on the lifespan of the worm, C. elegans, which eats E. coli as food.Mutations in different strains of E. Coli increased the lifespan of the worms that ate the mutants. Evidence is presented that a secreted metabolite made within the mutant bacteria, colanic acid, increases mitochondrial function in the worm to promote their longevity. That's pretty amazing and offers a very intriguing hypothesis that healthy bacteria in our gut could be providing us with anti-aging metabolites.

A few other nuggets of interest:

-Scientists have extended the ability to transmit and identify entangled particles at a range of 1200 kilometers using satellite transmission: per their report, this could be the beginnings of a new communication network.

-On a similar note, researchers have published on a new method to conduct wireless power transfer. I won't even attempt to explain the math or the technical garble in this paper, but the results here are a new avenue to remotely power objects across potentially large distances. Really cool!

-Scientists have published the structure of the cytomegalovirus virus (CMV). This virus is quite common in humans and can impact our immune response as we age, not to mention the virus is responsible for a host of other conditions. The virus is also related in shape to the herpes viral family and may offer new insight in combating herpes.

-We are a few steps closer to exoskeletons that could assist humans with work or help those with disabilities regain mobility. This new model helped humans with walking and running and load-bearing tasks!

And last of all, a new report assessing the potential global impact of climate change on a county-to-county level in the United States. It's a very necessary first step in combating the pseudoscience and false beliefs about the impact of our warming world and it does a fair job at applying economic forecasting to project county GDP and mortality rates by the end of the century. The model accounts for changes in county GDP for each 1 degree rise in mean global surface temperature, and no surprise that the southeastern portion of the United States would take the brunt of the impact.

That's partially due to the susceptibility of the south and east coast to damage from major storms, rising ocean levels, and decreases in crop yields during long periods drought and heat. However, the model also tries to adjust for local temperature changes, social unrest, and other demographic factors that can influence response to climate change. The model doesn't account for how migration and new technologies may impact the U.S., nor does it take into account major international changes that could also influence county-level differences in the long-term. However, the authors are developing future models that incorporate those important factors. Either way, it's not good news if you live in the south, east, or the Midwest!

That's it for now, have a great Fourth of July!

Wednesday, June 7, 2017

SciDay: Science in April and May (and Today!)

It's been quiet on the blog for the last few months. That's partially due to laziness, partially to a crazy schedule at work and at home. I've also been writing fact articles for the science fiction webzine Cosmic Roots and Eldritch Shoreswhich can be found on their Science News and Information blog here. My first articles have focused on the scientific method and the amazing potential of open access data. If either of those topics interests you, I suggest you pop over and take a look! I'll be posting there regularly in the coming months. 

I've also been reading slush for Cosmic Roots and Liminal Stories, which if you're unfamiliar, means I first-read new science fiction and fantasy submissions to these magazines. It's been an incredible learning process for my writing and I'm getting a chance to read some great short fiction. I've picked up a few nuggets of wisdom along the way about submitting short stories and I'll try and summarize them in another post later this summer after I collect my thoughts. 

But enough about that, it's time for some science! Researchers have made some major breakthroughs in April and May. I'll highlight just a few of them.  

There has been a controversial addition to the working theory of when humans and/or human-like species first arrived to the American continents. In January, it was reported that humans had a presence in North America as far back as 24,000 years (10,000 years earlier than previously believed) when bone fragments were discovered in the Yukon Territory. In April, a study in Nature revised these estimates by at least 100,000 years to over 130,000 years ago! Archaeologists examined an ancient site in California where mastodons were butchered and prepared for food with tools, including stone hammers and anvils, used to break open the bones for the marrow. More studies will be needed to confirm the findings in California, but if this can be validated this may cause us to re-think human migration into the Americas entirely. 

Update: Even more interesting, a study published earlier today (June 7th, 2017) in Nature has potentially pushed back the date of when the first humans ever appeared on Earth. Until recently, the oldest known human fossil was from about 200,000 years ago. But a discovery in Morocco has challenged this and pushed the date back potentially as far as 300,000 years ago. Wow.  If that doesn't cause shockwaves in our understanding of our species, I don't know what will.

Okay, next on the list of breakthroughs: vampires! Not really, but close enough. 

For the last decade, researchers studying the process of aging have examined the effects of using young blood as an anti-aging therapy. Blood isolated from young mice and administered systemically to older mice rejuvenated muscle and liver tissue in older mice. Since then, there has been a race to identify the specific factors associated with this renewal process. Back in April, researchers from Stanford published a study showing that continual administration of human cord blood (blood isolated from umbilical cords) into older mice could rejuvenate the hippocampus and improve cognitive function and neuronal activity. A protein found in human cord blood, called tissue inhibitor of metalloproteinases 2 (TIMP2), is believed to be actively contributing to this process. 

This is pretty incredible. A specific factor has been identified that drives this change and could potentially lead to anti-aging therapies by administering TIMP2 into the bloodstream to protect against age-related cognitive decline. And while this may be as simplistic approach to anti-aging therapies, we're on the cusp of finding additional factors that also contribute. Obviously there are a lot of ethical concerns using this approach in humans and these studies need independent validation, but I can't help but think of the medical benefits. Perhaps there will be a True Blood-like cocktail for humans in the coming years and we can all live to be 200? I'm sure vampire enthusiasts will love that.

Next up, a few tidbits here and there that I found interesting:

-A new report on the 3-D structure of all genomic DNA in a single nucleus from a single cell in mice: this could help identify important DNA domains and regulatory regions that control gene expression, cell functionality, and ultimately provide insight into what happens to a cell as it ages or turns cancerous. Below is a picture of how Chromosome 10 in mice is individually folded, and how that fits with the other chromosomes in the nucleus. Really awesome stuff!




-No surprises here but low-income Americans experience the most disparity in expected life-span and have the poorest health outcomes in the US: the gap in health disparities widened between low-income and middle-income Americans during the last 40 years. This paper is part of a series on healthcare in America. If you hit a paywall on this, let me know and I can point out other resources for you of you're interested in reading more about income and health disparity in America. It's sad.

-CRISPR strikes again: a tweak to the CRISPR-Cas9 gene editing system, this time replacing the Cas9 protein with Cas13a/C2c2 (a related protein), can help clinicians accurately identify Zika or Dengue fever infection using CRISPR technology as a diagnostic tool. This is really awesome and once it's perfected, it could be incredibly useful combating diseases across the world...particularly in those countries with fewer resources to tackle health-related issues. This new technique still has much to address with respect to cost and feasibility, but it's a great idea, and may even prove possible for use in the field during an outbreak.

-Important work was published in May that addresses climate research inconsistencies, particulary with respect to the 'global warming hiatus' that is often cited by climate change deniers: these data identify factors that influenced the idea of a long-term hiatus in global warming, including analysis of dataset usage and the use of differing definitions of the word hiatus. The authors argue that the presence of a hiatus is over-exaggerated for politically-motivated benefit.

-Cephalopods, including cuttlefish and octopi, have evolved a unique way to edit their own genomes: this branch of the animal kingdom predominantly increases protein diversity using RNA editing, as opposed to evolutionary selection of mutations arising in their DNA. This means that these animals evolve very slowly on a generational level, but are able to adapt individually to their unique environment much more rapidly...even perhaps using real-time RNA editing to respond to short-term problems or needs. That's really fascinating, and highly unusual, and I hope more research studies this mechanism.

And to wrap up:

In May, I was able to attend the Nebula Awards convention and the week after I went to Balticon, Baltimore's Science Fiction and Fantasy convention. I had an amazing time meeting many new people, including fantastic writers and editors and general fans of SF&F. At Balticon, I presented two seminars on my own research on aging and health disparities and it was a real treat. I wanted to say thank you to all the organizers of these events and for the invitation to speak at Balticon.

As well, a big Congratulations! to all the winners and nominees at the Nebula Awards this year. All of the nominated works were very deserving and the literary talent in the room was so energizing. One person I'd like to mention is Dr. Kjell Lindgren, pictured with me below, who is a NASA astronaut and physician.



Dr. Lindgren was the guest of honor and toastmaster at the Nebula convention. During the awards ceremony, he gave a wonderful speech about space flight and what it's like living aboard the International Space Station. He also sat on panels throughout the weekend and shared his insight about space travel and its impacts on the human body.

It was so inspiring to see someone so clearly passionate about science and so supportive about the benefits of science research. I look forward to reading more about his travels in space in the years to come, including all the research he does with NASA. He's doing great work on how the human body responds to long-term spaceflight and how we might be able to protect the body as we send astronauts back to the Moon and to Mars. AWESOME!

Well, that's it for now. Cheerio folks and thanks for reading! Drop me a line, anytime.

Friday, March 31, 2017

March SciDay Friday!

Well, we're a quarter of the way through 2017 and what a year it's been for science so far! There have been some challenges, and even more challenges, and for a change of pace, more challenges. It's incredibly frustrating and the War on Science has only just begun. But today, let's primarily focus on some of the victories. I neglected to post a monthly update last month, so today's post will be a conglomeration of science published predominantly in February and March.

I'm also excited to announce that I'll be posting regular blog posts for the science fiction magazine Cosmic Roots and Eldritch Shores. Cosmic Roots is a new magazine featuring science fiction, fantasy, and other short stories. I'll be contributing as often as I can on fact-based articles about science and society. I'll be sure to link my posts here as well, as many of the posts will be open access and free. Interviews and other types of articles I may write will be for subscribers to the magazine and if you like reading science fiction short stories it is worth getting a subscription.

Okay, so what's been happening in the world of science?

There has been considerable attention on the environment lately, which should come as no surprise given how important our climate is to our health and sustainability as a country and planet. Last month, researchers in Germany published a comprehensive report on oceanic oxygen content and reported a 2% global decline in oxygen levels in the ocean since at least the 1960's. The levels of decline were variable by region and depth and a handful of areas even saw an increase in oxygen content. This type of comprehensive assessment is very important given the link between ocean oxygen levels and aquamarine health. If oxygen levels in the deeper parts of the ocean continue to drop as projected, the reduction in diversity of life and resources provided by our oceans will greatly impact society.

For example, water oxygenation is important for plant life and coral reef health in coastal environments. Another recent study found that seagrasses in coastal regions can reduce pathogenic bacterial populations in coastal ocean waters that are harmful to humans and sea creatures, alike. This is important evidence that healthy seagrass meadows sustain a ecosystem that has direct benefit to human health along the coasts (where a majority of humans live) and this is linked to the oxygen levels in the oceans. This balance will be vital to study and protect.

Physics has also had some remarkable discoveries and advances. Of course, the 'big one' was the discovery of seven planets that orbit the dwarf star TRAPPIST-1. TRAPPIST-1 is roughly 40 light-years away, so we won't be heading over to check it out anytime soon. However, each planet is close enough to the dwarf star that it could be warm enough for liquid water, and perhaps even life. This is a monumental discovery, as there are now known and nearby solar systems that could be hospitable for humans or other forms of life. Identifying this system gives researchers the opportunity to study how solar systems like ours formed, the requirements for liquid water on planets orbiting stars that are different from the Sun, and if these planets have any atmospheric conditions that support life...perhaps even if they contain oxygen. It's time to fire up the generation ships.

On the other end of the physics spectrum, researchers in Vienna have provided the first proof-of-principle experiment that confirms important aspects of quantum entanglement. Okay, what the hell does that even mean? In a nutshell, quantum entanglement suggests that some information can indeed travel faster than the speed of light. If two particles of matter become 'entangled', no matter how far apart you separate them, whether it's across a town, or galaxy, or the universe...what you do to one particle will automatically influence what happens to the other particle, regardless of the distance between them. Is your mind blown yet?

It's a lot to take in and I'm admittedly not the best source of information on this. The Atlantic has a very good article about what entanglement really is, the importance of this breakthrough, and Einstein's thoughts on 'spooky action at a distance', as he called it. I suggest checking it out as it explains everything very well.

Switching gears over to biology, I found some interesting articles I thought were worth bringing to your attention. DNA Fountain was just announced, the most current platform available to store data and information in strands of DNA. DNA Fountain was able to perfectly record, code, and decode movies and digital files (up to 2.5 Mb) in strands of physical DNA. While the sizes of these files isn't really impressive, the scalability of the DNA Fountain is the innovation being reported, with a maximum potential of up to 680 petabytes of information stored using this method. To put that into perspective, some of the largest, commercially-available external hard drives can store about10 terabytes of data....so a single gram of DNA could theoretically store 680,000x more information. Cost efficiency is a concern at this point, as is error-free recording, but the future of information storage may very well be using our own genetic code. Very cool.

Speaking of DNA, it's long been known that as we grow older we accumulate more DNA damage and mutations in our cells. DNA mutations can be caused by environmental exposures (such as UV radiation or from carcinogens found in cigarettes), errors in DNA replication when a cell divides, or even the stochastic process where some DNA nucleotides will spontaneously turn into another (this is called DNA deamination). In my opinion, the accumulation of DNA mutations can lead to predisposition to many diseases, but that can be hard to accurately assess. In fact, there is still an ongoing debate as to how much age-related mutations contribute to the onset of  diseases, like cancer. The latest paper by Bert Vogelstein at John Hopkins attempts to address that issue in cancer. His laboratory is reporting that of the three ways DNA mutations can lead to cancer (1. through inheritance; 2. via environmental exposure; or 3. errors in DNA replication during cell division), random errors in DNA replication explain nearly two-thirds of all cancers.

This is a very provocative paper and assuredly cancer researchers are going to go to battle over this data. If correct, it means that a majority of cancers are caused at random and may not be preventable...some researchers are simply calling it bad luck. This has implications for prevention and therapy and it does agree with the history of studying cancer, in that cancer is now seen as a complex variety of conditions dependent upon the type of mutation driving the cellular growth and the tissue of origin. This finding also means a lot of work is going to be needed in the future to make cancer prevention and treatment more personalized so that those who develop cancer survive and with as few side effects as possible.

The last paper I'll highlight is a study of predicted life-expectancy in 35 industrialized countries around the globe. No surprise, the United States is projected to have one of the lowest gains in life expectancy in the developed world. With some of the failures in the Affordable Care Act and the new Administration's growing War on Science, particulary the idiotic ambitions to drastically reduce the science and health research capacity in the United States, this issue will undoubtedly become more important and apparent in the coming years. The authors of the report put it best and I'll just place their comments right here:


"Notable among poor-performing countries is the USA, whose life expectancy at birth is already lower than most other high-income countries, and is projected to fall further behind such that its 2030 life expectancy at birth might be similar to the Czech Republic for men, and Croatia and Mexico for women. The USA has the highest child and maternal mortality, homicide rate, and body-mass index of any high-income country, and was the first of high-income countries to experience a halt or
possibly reversal of increase in height in adulthood, which is associated with higher longevity. The USA is also the only country in the OECD without universal health coverage, and has the largest share of unmet health-care needs due to financial costs. Not only does the USA have high and rising health inequalities, but also life expectancy has stagnated or even declined in some population subgroups. Therefore, the poor recent and projected US performance is at least partly due to high
and inequitable mortality from chronic diseases and violence, and insufficient and inequitable health care."

But the best strategy is definitely to reduce federal research support for these important issues...blah!

Other tidbits:

-Apparently there is going to be a big dustup in the dinosaur world. Last week a study in Nature was published that called for an entire reorganization of the classification and naming of Dinosaurs. Hopefully the Brontosaurus returns! If any dinosaurs feel chumped by how things shake out, they can certainly phone a friend in Pluto.

-Early in human history, some of our ancestors interbred with Neanderthals and remnants of the Neanderthal genome are found in certain human populations. This month another study was published that provides evidence that genetic elements humans inherited from Neanderthals are functional and contribute to human phenotype variation (not all humans have Neanderthal ancestry!).

So there you have it. Until next time, enjoy Spring!

Tuesday, February 14, 2017

Thoughts On My March for Science

Many scientists have already publicly announced their support for the March for Science that is going to take place on Earth Day, April 22nd, in Washington D.C. and across the nation and world. I've already declared my intentions to join in, but the more I've thought about why I'm marching, the more I've realized I want to explain myself to anyone with the care to read this. (I'm also well aware of the fact that is already almost cliche to be a scientist posting on a personal blog about why the March for Science is important. But alas, the opportunity to talk about science and the fact that scientists and science supporters are coming out from the woodwork to unify around the idea of a free and informed democracy is too good a chance to pass up!)

A few points I'd like to clarify before getting into the heart of this matter. First, not everyone agrees that there should be a march, while others have offered advice on how to make the most impact. Each of these articles discusses some very important points and in each case it's mentioned that there is a danger that this movement will become politicized and partisan and this will negatively affect the overall impact and message. This is very important and their advice and commentary should be heeded by everyone attending (and especially those who are organizing).

This event must not become a political partisan issue primarily because science in general is NOT a partisan issue. Science interacts with everyone in this nation, everyday. While my previous point may sound trite, it really is the core at which how our world works.

You can find a broad list of goals and messages about the March for Science on their website, so I'm not going to dive into them. I'll just say in general I agree with the over-arching summary and most of the organizers' points, though not necessarily the ordering of those points (which I am assuming is listed top-down for emphasis, and if they aren't in any particular order I really hope the organizers will make a point of that on their webpage). Several of my points certainly overlap with theirs on a variety of levels, but these are the ones that speak most to me as an individual.

So, personally, what am I NOT marching for?

I am NOT marching for increased funding for my salary, or anyone's salary in science.

I am NOT marching to convince anyone that science will solve all our problems as a country.

I am NOT marching to further divide our polarized country.

So, personally, what AM I marching for?

1. Continued access to, and increased awareness of, the scientific process, how that creates new information, and engagement with anyone on why that information is fundamental to a sustained democracy.

2. Increased awareness about what science can do for the public good and how that will benefit everyone in society, regardless of religion, race, socioeconomic status, political party, gender, and sexual background.

3. Convincing other scientists that communication is a skill that needs training and development, starting at the undergraduate level.

4. Shifting the paradigm away from the dichotomy of scientific thinking some scientists have that there are scientists and then there is the public.

As a government scientist I feel it is my duty to make sure that everyone I know is aware about these reasons and my thought process behind them. My research and job are funded by your tax dollars and you have a right to know why I am taking these issues seriously. Also, I have dedicated my life to trying to increase humanity's knowledge about the world, as well as educating the next generation of scientists on the best practices to answer more questions and further increase that knowledge. Those endeavors are at the core of who I am and drive me to both write this post and walk on the streets of Washington D.C. to discuss this with anyone who is willing to listen.

I'd like to take the rest of your time to highlight some important points about each of the ideas I just put forth:

I am NOT marching for increased funding for my salary, or anyone's salary in science. I have already marched four years ago advocating for an increase in NIH funding. I'm not interested in my own salary, but rather a general increase in financial support for more labs and more experiments to study medicine, space, technological innovation, materials science, basic biological and behavioral research, food science, climate research, geological work, and others. All of those areas provide a benefit that supports our economy, our position as a leader in the free world, and help better improve the lives, health, safety, and protection of all us in this country and beyond.

I am NOT marching to convince anyone that science will solve all our problems as a country. I will not go into much detail here other than to admit that science will not solve all our issues. Science is a process that often takes time to come to the right solution or answer. Sometimes in science, like in life, an answer just isn't possible. But research CAN increase our potential as a society to solve large and complex problems. Many who do not understand how the scientific process works use this as an example to try and undermine how important the scientific process is and why disagreements among scientists about particular issues are an important aspect of that process (perhaps I'll write on this later). Please don't let these individuals sway your views on what good science can do for the world.

I am NOT marching to further divide our polarized country. Science impacts all of us, whether you believe it or not, or whether you care or not. I think it really hurts the democracy of our nation if science becomes politicized across party lines. There are many individuals on both sides of the aisle that can and will try to polarize these issues. The basic issues of information exposure, truth about how the world works, and how we might be able to implement good policy from that information are fundamental issues both Democrats and Republicans support, have supported in the past, and will continue to support in the future.

I AM marching for...continued access to, and increased awareness of, the scientific process, how that creates new information, and engagement with anyone on why that information is fundamental to a sustained democracy. 

An informed democracy and Congress can make better decisions. This relates to predicting the next earthquake or drought; when and if a new virus will jump to the Americas; how we can engineer our aging infrastructure; what space medicine can tell us about our own health down on the ground...the list goes on. There is a process involved with studying and publicizing this information that I will try to discuss leading up to the march and after. This includes peer review, funding, communication, and other aspects of the research enterprise.

All of this is of course related to education and access to information. Currently there are a handful of bills working their way through Congress that will limit your tax-paid access to basic information that may contribute to your education in the future, understanding your impact on the environment and how we can respond to it, your cyber security protections as a patient, or even allowing politicians to influence how basic science research is performed. There are some great bills as well that should be celebrated, such as the REAL Space Act to send us back to the Moon. In an age of post-truth and disbelief in fact, the only way to increase our potential as a nation is to keep discussing what is really impacting our world and why that should matter.

I AM marching for...Increased awareness about what science can do for the public good and how that will benefit everyone in society, regardless of gender, religion, race, socioeconomic status, sexuality, or political party.

I don't think I'll explain this one too much as it seems self-evident. However, if you are interested in how we can use data to understand our world better and begin to address disparities in a meaningful way, I'll direct you to this intuitive and free program where you can explore the disparities in our world. Our country is full of diverse people and varied experience and that makes our country strong. However, it means populations can be marginalized, discriminated against, and ignored. Sometimes this is intentional and other times it's not. Generating new data about these issues in our own country will greatly increase our chances of solving public health and societal crises like gang and gun violence, epidemics, and basic access to clean water and safe food, education, and opportunity. Data can help play a role in helping those who need government and societal attention the most. This is a fundamental core value of our country and science is an ally to this endeavor.

I AM marching for...the need to convince other scientists that communication is a skill that needs training and development, starting at the undergraduate level.

This is more relevant to those in my profession. Scientists can be horrible communicators and educators and this has to be addressed if science is going to continue to move forward in a productive way in this country. New strategies are needed to enhance early-career scientist training on issues of data communication and discussion...both within the scientific community and outside of it. Thankfully, new initiatives by the NIH and elsewhere are looking to enhance this for graduate school training, but more work is needed and at younger ages. The idea of communicating our research effectively to 'non-scientists' is also aligned with my fourth goal....

I AM marching for...shifting the paradigm away from the dichotomy of scientific thinking some scientists have that there are scientists and then there is the public.

There are so many people in this country who are interested in science and looking to do more with it in their lives who are not scientists at all. Scientists can often come off as arrogant and unapproachable, I'm guilty of this at times, and this can be an impediment to very important conversations that need everyone in the country to weigh-in on. I'm marching to increase that conversation and eliminate the perception in the scientific world that our work can't be understood by everyone. This is wrong and unfortunate and with proper training every scientist can and should be able to explain their work to anyone. Breaking down this dichotomy can help with this process and make data more approachable.

So there it is. That's why on April 22nd you'll find me in Washington, D.C. I hope you come as well because this issue will impact everyone and will help shape our discussions moving forward.

Tuesday, January 31, 2017

January's SciDay!

I've got one day left to keep up my tradition of commenting on each month's scientific breakthroughs. Since I've been teaching all month for the Citizen Science Program at Bard College (an amazing experience by the way), I've had almost no time to catalog and write about some of this month's interesting research papers. So last night in a flurry of activity I found a few things of particular interest and which I'll quickly summarize below:

Last month I commented that some natural compounds had been found that inhibit the CRISPR/Cas9 immune system in some bacteria. This is of note because this may be a natural way to better control human genome editing initiatives using CRISPR technology. This month, researchers at the University of California in San Francisco have identified in the genomes of phages (viruses that infect and kill bacteria cells only) a new set of inhibitors that target the CRISPR/Cas9 system in the pathogenic bacteria that cause listeria. These newly identified inhibitors also prevent CRISPR from working properly in human cells, too. As an added bonus, the study of these new molecules may help researchers explore novel ways to kill bacteria that are resistant to antibiotics. I learned during my time teaching at Citizen Science that the use of phages was widespread during WWII in Russia and elsewhere in order to combat bacterial infections on the battlefield. Phages were used in lieu of antibiotics...which weren't always readily available. Dr. Paul Turner at Yale (who also spoke at Bard this month and got me thinking about this) studies the use of viruses as a way to combat bacterial infections, especially against antibiotic resistant bacteria. (*Check out this link if you want to know more about it!*)

In my mind it is conceivable to engineer new phage viruses, with the genes coding for CRISPR inhibitors genetically engineered into their genomes, to be used as a new generation of viral drugs targeting antibiotic resistant bacteria. These viruses would then be resistant to the defense system of those bacteria and may be better at killing them in humans with bacterial diseases. Lots to mull over, but I think this could be very promising and I'll keep an eye out for research about this (if it doesn't already exist).

Additionally, what's really exciting is that this week researchers in Israel identified a new communication system between phages that help the viruses decide, upon infection of a bacterial cell, if they will kill the bacteria fast or enter the bacterial genome and go into a quiet, inactive state (called lysogeny) and kill the bacteria later. This is an incredible discovery and indicates that viruses are yet again more complex than we thought and capable of very simple communication. It was found that the genomes of distinct viruses have unique genes that code for small peptides and these small peptides are the messengers in this communications system. Think of the peptides as little hormones that tell the viruses when and if to kill the bacteria cell immediately upon infection, or later.

This of course opens the door to looking for these types of messengers in viruses that infect humans, and if they are indeed present, this may open up an entirely new avenue to explore for anti-viral therapy to save human lives. Now, that's A LOT of if's, but I'm feeling positive today and I hope this becomes a major breakthrough in our understanding of viral infections.

Next month I'd like to discuss some new announcements in NASA's Twins Study results. This is a study that is comparing the genetics and physiology of two astronauts after one of them, Scott Kelly, spent almost a year in space while his identical twin brother, Mark, stayed back on Earth. Scientists and clinicians are trying to better understand how space affects the human body. It's awesome research, with some ethical considerations that I'll get into next month.

I'll leave you with this: The Art of Saving a Life. This is an initiative by the Bill and Melinda Gates Foundation that brought together artists, poets, writers, film makers, and others to promote vaccine awareness using art as a medium. There is some incredible and beautiful art on this website, including some very moving and powerful short films. I wanted to highlight this here as an example of how anyone can help promote the cause of science (not just scientists) as a tool to protect and help people, promote awareness on this issue and others, increase our knowledge of how the world works, and encourage and support informed government policy.

Until next time, Go Spurs!

Tuesday, January 24, 2017

My Belief in Science and Truth in the Era of Trump

It hurts my heart that the current administration is engaging in deceit, falsehoods, and inaccuracy…and it is not even a week into the current changes. I work for the United States government and already many like-minded individuals and scientists are under governmental restriction to remain silent about simple facts of our world. I am fortunate to remain mostly outside of those restrictions…at the moment.

This form of silencing is reminiscent of governments in countries that rule by fear, devalue free thinking, and fuel propaganda. As a scientist and employee of the National Institutes of Health, I feel it is my duty to provide the most accurate truth that is available in the effort to educate and protect those that rely on accurate health information and fact…particularly those groups that are underrepresented in science.


Perhaps I’m looking at the dark side of the moon; perhaps I am overreacting. Both are possible, I’ll admit. But I promise to myself and my family and friends and to everyone else that I will not allow myself to be subjected to falsehood and the belief that there are ‘alternative’ truths to basic facts and truth. I feel incredibly passionate about this and I will not be dissuaded from engaging anyone, on either side of the aisle, from a productive discussion about these principles so long as people are willing to acknowledge that there is a reality to our world that can be defined in a reasonable way. This is dramatic maybe, but I feel this is imperative to define for myself and those I know as our country moves forward.   

Friday, December 30, 2016

December's SciDay Friday!

It's the last Friday of December and that means one final chance to talk about some science from the month. I'm only going to highlight four papers today, mainly because I didn't prepare this month's post as much as I typically do. Damn you, cookie-induced comas. But if you want to read more about the science from all of 2016, check out this Nature News Feature highlighting ten scientists who were vital this year. Not to be outdone, Science News has a rundown of their own.

The first paper can be found in Science Translational Medicine and explains some of the coolest science being performed right now. Researchers in Boston have developed a personal cancer vaccine for patients who suffered from acute myeloid leukemia (AML). Leukemia cells were isolated from patients with AML and fused together with dendritic cells (a type of immune cell that creates antigens which help the immune system recognize the stuff that shouldn't be there, like viruses and other cancer cells). These hybrid cells, part cancer and part immune, were injected back into AML patients who were in remission after successful chemotherapy treatment. The idea is that these hybrids would teach the other immune cells in each patient how to recognize the antigens from their own cancer and help them root out any leukemia cells that survived chemotherapy...thereby preventing recurrence of their cancer. Twelve of the seventeen patients have remained relapse-free for over four and a half years! Although some patients did relapse after this therapy, the rate of success warrants a closer look at this approach as a means of combating relapse or even as an initial treatment of metastatic cancers. The technology will need to be refined but this proof of principle in actual cancer patients is an awesome development.

The next paper investigates how animals experience time and I have to say, it's about time I started talking about time considering this blog is called Ripples in Time. Researchers in Portugal used drugs and optogenetics to manipulate midbrain dopamine neurons in mice to identify changes in their perception of time. (Quick refresher: Dopamine is a neurotransmitter that is involved with reward and behavior [among other functions] and optogenetics is the manipulation of the function of cells in live animals using fiber optic cables and light.)

Researchers found that dopamine neurons in the midbrain are directly involved in judging periods of elapsed time, either when the neurons are stimulated to release dopamine or suppressed. Since neural circuits are way beyond my expertise, I'm going to quote the end of this article to get the point across. The writing in brackets are my own to help clarify:

"Situations in which DAergic [dopamine neuron] activity is elevated naturally, such as states of high approach motivation, response uncertainty, or cognitive engagement are associated with underestimation of time. Conversely, situations that decrease DAergic activity, such as when fearful or aversive stimuli are presented, are associated with overestimation of time. These observations, together with our data, suggest that flexibility in time estimation may confer an adaptive advantage on the individual." 

This is direct evidence that the neuronal activity of some of the dopamine neurons in animal brains directly affect how we experience the length of time of events. So when I went to see Star Wars Rogue One I didn't even notice the movie was over two hours long because I was so excited while watching...whereas when I vacuumed the house earlier this week it felt like it took forever because my 'cognitive engagement' was low. Our perception of time is directly related to how stimulated we feel. This is cool stuff and may suggest how different people experience the timing of the same events in different ways. The results of this study also implied that the changes in perceptions in time were altered on the scale of actual seconds. This got me thinking. Maybe it isn't the Force that gives Jedi their ultra-fast reflexives, just really efficient dopamine neurons. But I digress... 
 
The third paper is an oddball, which I've tried to incorporate into each of these posts. Scientists in Europe used satellite data to measure changes in land surface water over the entire globe between 1984 and 2015. The satellite imagery had a resolution of less than 100 feet, which is pretty incredible, and this a first of its kind survey. A few summarized points of the findings:

-Globally, land-surface water has increased almost 94,000 square kilometers (about the size of Lake Superior, according to the researchers)
-The addition of this surface water is evenly distributed among the continents and linked to locations with reservoir building, dam construction, and are perhaps even influenced by changing local climates
-Over 70% of surface water loss was concentrated in the Middle East and Central Asia and linked to drought, river diversion and other human activities

I wanted to highlight this paper for a variety of reasons. I agree with the authors that this type of open-source mapping of available water resources is essential for the sustainability of clean and available water in the future. I think it is also smart to recognize that water loss and gain is influenced by human activity, drought, and maybe even the changing global climate, and charting the areas where the greatest changes are occurring can help predict areas that will need help in the future. Imagine in thirty years if the Middle East and Central Asia lost almost all of their surface water and the problems that could pose socially and politically. 

My main problem with this paper is that the authors try to present this data and incorporate their own commentary on climate change. I think that climate change is inherently a major influencer of water availability in our world...it would be foolish not to think so. But the presentation of this data, particularly in the abstract, was written in such a way to first highlight the loss of global surface water and gloss over the fact that surface water actually had a net gain. I felt it was poorly worded and emphasized the wrong aspects of the data - the most important findings being the location and availability of surface water and where in the world changes in local climates (droughts) and human activity (dams) play a major role in this critical resource's availability and its management. It's a small, nit-picky critique, but it rubbed me the wrong way.

Oh well.

The last paper focuses on CRISPR (again!). I've talked about this technology in my last few posts and I feel it is so important that everyone understands the implications that I'm going to close my 2016 discussion about this topic. This time I'd like to feature a paper that came out in Cell and identifies natural compounds that inhibit Cas9, the essential enzyme component in the CRISPR gene editing system. Remember, the CRISPR system is a type of naturally-occurring immune system for bacteria which is applied against invading viruses that infect those bacteria. Inside the CRISPR gene system for the bacteria Neisseria meningitidis, researchers found three genes that code for proteins that inhibit the activity of Cas9 and therefor the CRISPR system. Several genes, related in function, are also found in the genomes of bacteria-infecting viruses. Together, this means that viruses have evolved a way around the CRISPR system and now those genes are being shared (and evolving on their own) between bacterium. 

The great news is researchers now have a way of inhibiting the CRISPR gene editing tool in animal cells with a natural protein found in bacteria. These proteins can be used as a drug/brake-system to limit off-target effects of CRISPR usage, protect specific tissues from being edited, and a way to prevent unforeseen downstream complications that may arise when using the CRISPR system in humans. I've long been concerned with the lack of restraints on the usage of CRISPR technology but the discovery and use of these enzymes is a step in the right direction with respect to control and safety. 

Wooo hoo! #science.

So that wraps up 2016. When I'm finished with teaching in January I'll write a few detailed posts about some controversies in science...starting with the reproducibility crisis. Until then, I wish you all a very wonderful and happy New Year and a great 2017!